I'll see if I can try it with my Mega later.
... Later ...
I have a JRuby with JSSC program that I used to test something for a project in another Thread. It sends an S Cr Lf sequence to the Arduino which responds with :nnn where nnn is a sequential count.
It worked completely unchanged on my Mega. I just plugged out my Uno, plugged in the Mega and uploaded the sketch. And started my JRuby program and it just worked.
I'm using Ubuntu 12.04 and "java version 1.7.0_17". I have the Java JDK installed.
...R